+Open data
-Basic information
Entry | Database: PDB / ID: 5fbv | ||||||
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Title | PI4KB in complex with Rab11 and the MI364 Inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / Inhibitor / Complex / Kinase / Lipid | ||||||
Function / homology | Function and homology information regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / melanosome transport / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / astral microtubule organization / VxPx cargo-targeting to cilium / protein transmembrane transport / Synthesis of PIPs at the Golgi membrane / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / dynein light intermediate chain binding / protein localization to cilium / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / cleavage furrow / inner ear development / centriolar satellite / mitotic spindle assembly / transport vesicle / vesicle-mediated transport / phagocytic vesicle / 14-3-3 protein binding / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / receptor-mediated endocytosis / small monomeric GTPase / G protein activity / regulation of cytokinesis / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.285 Å | ||||||
Authors | Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
Citation | Journal: To Be Published Title: PI4KB in complex with Rab11 and the MI364 Inhibitor Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbv.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbv.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbv ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbv | HTTPS FTP |
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-Related structure data
Related structure data | 4d0lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65264.766 Da / Num. of mol.: 1 / Fragment: UNP Residues 128-422, 523-799 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB / Production host: Escherichia coli (E. coli) References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase |
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#2: Protein | Mass: 24813.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491 |
#3: Chemical | ChemComp-5W3 / ~{ |
#4: Chemical | ChemComp-GSP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15M amonium sulfate, 0.1M MEW pH=6, 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.28→46.97 Å / Num. obs: 14745 / % possible obs: 99.01 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.63 / Num. measured all: 50723 |
Reflection shell | Resolution: 3.28→3.4 Å / Mean I/σ(I) obs: 0.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D0L Resolution: 3.285→46.966 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.285→46.966 Å
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Refine LS restraints |
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LS refinement shell |
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